|
Status |
Public on Feb 12, 2019 |
Title |
Male 20 min digestion SSP |
Sample type |
SRA |
|
|
Source name |
Male F123 mESCs from Cast/129 backgrond
|
Organism |
Mus musculus |
Characteristics |
strain background: Cast/129 Sex: Male cell line: F123 cell type: mES cells
|
Treatment protocol |
Nuclei are isolated and treated with a limited amount of micrococcal nuclease for a specific amount of time
|
Growth protocol |
Cells are grown under standard mESC culture conditions (15% FBS, serum + LIF, 1X Pen/Strep) on 0.1% gelatin (following two passages on mitotically inactivated MEF feeders)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells are lysed using a standard phenol-choloroform-isoamyl alcohol purification Mnase-SSP is performed using the single-stranded library prep of Gansauge and Meyer (Nature Prot. 2013) Libraries are sequenced with a custom read 1 primer on Illumina MiSeq or NextSeq instruments
|
|
|
Library strategy |
MNase-Seq |
Library source |
genomic |
Library selection |
MNase |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
ML_20 Male F123 mESCs from Cast/129 backgrond
|
Data processing |
library strategy: Mnase-SSP Reads were mapped to a combined Burrows-Wheeler reference of mm10 using bowtie2. They were then filtered using custom Python scripts to generate deduplicated, sorted, indexed BAM files Genome_build: mm10 Supplementary_files_format_and_content: processed data are aligned, deduplicated, sorted, and indexed BAM files that all scripts in the associated GitHub account
|
|
|
Submission date |
Jan 14, 2019 |
Last update date |
Feb 14, 2019 |
Contact name |
Vijay Ramani |
Organization name |
UCSF
|
Department |
Biochemistry & Biophysics
|
Lab |
Ramani Lab
|
Street address |
600 16th St, GH-S312B
|
City |
San Francisco |
State/province |
California |
ZIP/Postal code |
94143 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE125053 |
High-resolution analysis of chromatin structure by Mnase-SSP |
|
Relations |
BioSample |
SAMN10741252 |
SRA |
SRX5247948 |